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Detailed information for vg0826333758:

Variant ID: vg0826333758 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 26333758
Reference Allele: GAlternative Allele: T
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.91, T: 0.09, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:


AATTACCACTGTCGAGAAAATATCTCGTTGTTTTTTCATATCATCTAAATAGTTATAAAAAAATTAATAATATAGATTAATATAAAATATATCATTTCAA[G/T]
ACAAACAAGACTAAATTCGACTTTTACAAATTAGAAAAAAAACAAATTAAACTTAAAATATTTATCGTACATCCGCATCTATATTTGTTTTTTTACAACT

Reverse complement sequence

AGTTGTAAAAAAACAAATATAGATGCGGATGTACGATAAATATTTTAAGTTTAATTTGTTTTTTTTCTAATTTGTAAAAGTCGAATTTAGTCTTGTTTGT[C/A]
TTGAAATGATATATTTTATATTAATCTATATTATTAATTTTTTTATAACTATTTAGATGATATGAAAAAACAACGAGATATTTTCTCGACAGTGGTAATT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 65.60% 33.10% 0.32% 0.93% NA
All Indica  2759 79.20% 19.00% 0.40% 1.49% NA
All Japonica  1512 41.30% 58.40% 0.07% 0.20% NA
Aus  269 86.60% 13.40% 0.00% 0.00% NA
Indica I  595 64.20% 35.60% 0.00% 0.17% NA
Indica II  465 85.20% 8.40% 0.65% 5.81% NA
Indica III  913 85.50% 14.50% 0.00% 0.00% NA
Indica Intermediate  786 79.50% 17.80% 1.02% 1.65% NA
Temperate Japonica  767 8.20% 91.40% 0.00% 0.39% NA
Tropical Japonica  504 86.30% 13.70% 0.00% 0.00% NA
Japonica Intermediate  241 52.70% 46.90% 0.41% 0.00% NA
VI/Aromatic  96 8.30% 91.70% 0.00% 0.00% NA
Intermediate  90 57.80% 38.90% 3.33% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0826333758 G -> T LOC_Os08g41720.1 intron_variant ; MODIFIER silent_mutation Average:64.902; most accessible tissue: Callus, score: 92.375 N N N N
vg0826333758 G -> DEL N N silent_mutation Average:64.902; most accessible tissue: Callus, score: 92.375 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0826333758 NA 3.33E-16 mr1301 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0826333758 NA 1.24E-06 mr1364 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0826333758 NA 2.58E-07 mr1443 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0826333758 NA 1.26E-06 mr1518 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0826333758 NA 5.78E-06 mr1532 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0826333758 NA 5.76E-10 mr1533 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0826333758 3.46E-06 NA mr1949 Ind_All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0826333758 NA 5.09E-11 mr1980 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0826333758 NA 4.94E-10 mr1993 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0826333758 NA 6.74E-07 mr1038_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0826333758 NA 7.48E-07 mr1248_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0826333758 NA 6.76E-07 mr1252_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0826333758 NA 9.10E-06 mr1263_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0826333758 NA 6.05E-16 mr1301_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0826333758 NA 9.01E-06 mr1603_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0826333758 NA 4.11E-17 mr1699_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0826333758 NA 3.16E-07 mr1874_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251